All metazoans examined to date contain repetitive DNA elements, and suggestions for their function include coordination of the expression of tissue-specific genes, promotion of chromosomal rearrangements such as duplications, inversions, and deletions, a role in speciation, or even no function except self-propagation as "selfish" DNA. We devised a semiquantitative method to analyze all the repeat DNA families of the rat and have identified a number of different classes: ancestral elements (i.e., those present in a number of rodent genera), elements specific to the genus Rattus, transcribed elements, nontranscribed elements, very high repeat elements, and divergent repeat elements. We are now examining the genomic organization of selected families corresponding to these classes and are constructing "chromosomes" in vitro containing one or more of these types of elements in an attempt to assess some of the functions that repeat elements serve in eukaryotic genomes.